OReilly sequence analysis in a nutshell a guide to common tools and databases jan 2003 ISBN 059600494x

[ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] dan program (EMBOSS) dasycladacean code databases BLAST, indexing CPGISLE, producing entry format reports DNA sequence, searching EMBOSS, searching for sequences with specified IDs or numbers PRINTS preprocessing for use with PSCAN PROSITE motif REBASE predicting cut sites in DNA sequences searching for restriction enzymes sequences, table listing ways to access dbiblast program (EMBOSS) dbifasta program (EMBOSS) dbiflat program (EMBOSS) dbigcg program (EMBOSS) DDBJ (DNA Data Bank of Japan) feature table [See DDBJ/EMBL/GenBank feature key table] flat files example field definitions locations [See DDBJ/EMBL/GenBank location examples table] DDBJ/EMBL/GenBank feature table DDBJ/EMBL/GenBank location examples table DDBJ/EMBL/GenBank qualifier table degapseq program (EMBOSS) description lines, FASTA descseq program (EMBOSS) dichet program (EMBOSS) diffseq program (EMBOSS) digest program (EMBOSS) dinucleotide CG, scanning for dinucleotides, determining number of in files distmat program (EMBOSS) DNA constructs linear maps of, drawing DNA Data Bank of Japan [See DDBJ] DNA double helixes, predicting bending of DNA sequence databases, searching DNA sequences displaying predicting cut sites in predicting twisting of domainer program (EMBOSS) domains coordinate files, writing from protein coordinate files dotmatcher program (EMBOSS) dotpath program (EMBOSS) dottup program (EMBOSS) dreg program (EMBOSS) [ Team LiB ] Brought to You by [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] > (greater than sign), FASTA : (colon), EMBOSS USA syntax | (vertical bar), Readseq formats [ Team LiB ] [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] AAINDEX database aaindexextract program (EMBOSS) ABI sequence trace files abiview program (EMBOSS) alignment formats, EMBOSS alignwrap program (EMBOSS) alternative flatworm mitochondrial code alternative yeast nuclear code amino acids charges to database of properties of properties summary amino-acid modifications SWISS-PROT feature table frequently used modifications lipid moiety attached groups antigenic program (EMBOSS) antisense, outputting application groups, EMBOSS ascidian mitochondrial code ASCII files, removing carriage returns from [ Team LiB ] [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] backtranseq program (EMBOSS) bacterial code banana program (EMBOSS) bases, searching sequences for Basic Local Alignment Search Tool [See BLAST] BioJava BioPerl biosed utility (EMBOSS) bl2seq program (BLAST) BLAST (Basic Local Alignment Search Tool) command-line options databases, indexing programs associated sequence types and server support for Readseq BLAST-Like Alignment Tool [See BLAT] blastall program blastpgp program (BLAST) BLAT (BLAST-Like Alignment Tool) blepharisma nuclear code btwisted program (EMBOSS) [ Team LiB ] [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] cai program (EMBOSS) carriage returns, removing from ASCII files cDNA sequences, producing from aligned protein sequences CGI web server, Readseq and change indicators, SWISS-PROT feature table chaos program (EMBOSS) charge program (EMBOSS) checktrans program (EMBOSS) chips program (EMBOSS) chlorophycean mitochondrial code ciliate code cirdna program (EMBOSS) ClustalW command-line options emma program as interface to codcmp program (EMBOSS) code, genetic alternative flatworm mitochondrial alternative yeast nuclear ascidian mitochondrial bacterial blepharisma nuclear chlorophycean mitochondrial ciliate coelenterate mitochondrial dasycladacean echinoderm euplotid nuclear flatworm mitochondrial hexamita nuclear invertebrate mitochondrial mold mycoplasma plant plastid protozoan scenedesmus obliquus mitochondrial spiroplasma standard thraustochytrium mitochondrial trematode mitochondrial yeast mitochondrial coderet program (EMBOSS) codes coding sequences, calculating codon frequency table from nucleotide Codon Adaptation Index, calculating codon frequency tables calculating from coding frequency codon usage table files coelenterate mitochondrial code coiled-coil structures, calculating probability of colon (:), EMBOSS USA syntax command-line options BLAST BLAT ClustalW MEME Readseq comments, FASTA compseq program (EMBOSS) cons program (EMBOSS) consensus sequence, calculating from multiple sequence alignment contacts program (EMBOSS) coordinate files reading writing protein-heterogen contact data files from CpG regions, identifying CPGISLE database, producing entry format reports cpgplot program (EMBOSS) cpgreport program (EMBOSS) crystalball program Ctrl-A characters, NCBI nonredundant database syntax cusp program (EMBOSS) cut sites, predicting in DNA sequences CUTG, extracting data from cutgextract program (EMBOSS) cutseq program (EMBOSS) [ Team LiB ] [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] EBI (European Bioinformatics Institute) echinoderm code einverted program (EMBOSS) EMBL (European Molecular Biology Laboratory) CD-ROM format index files building from BLAST database building from FASTA flat file database building from flat file database feature table [See DDBJ/EMBL/GenBank feature table] flat files example field definitions format files building from indexing GCG-format database converting SCOP classification files to writing SCOP classiciation to format SCOP files, converting to nonredundant files locations [See DDBJ/EMBL/GenBank location examples table] qualifier table [See DDBJ/EMBL/GenBank qualifier table] EMBOSS (European Molecular Biology Open Software Suite) alignment formats application groups data files, determining directories that can hold databases [See EMBOSS databases] feature formats help documentation for, displaying programs finding by keywords in documentation listing programs that share functionality with table of report formats sequence formats input output Uniform Sequence Address (USA) EMBOSS databases, searching for sequences with specified IDs or numbers embossdata utility (EMBOSS) embossversion program (EMBOSS) emma program (EMBOSS) emowse program (EMBOSS) entret program (EMBOSS) enzymatic data files, plotting eprimer3 program (EMBOSS) equicktandem program (EMBOSS) EST sequences, trimming poly-A tails off est2genome program (EMBOSS) etandem program (EMBOSS) euplotid nuclear code European Bioinformatics Institute [See EBI] European Molecular Biology Laboratory [See EMBL] European Molecular Biology Open Software Suite [See EMBOSS] extractfeat utility (EMBOSS) extractseq program (EMBOSS) [ Team LiB ] [ Team LiB ] [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] FASTA flat file database, indexing open source tools and feature formats, EMBOSS feature tables DDBJ/EMBL/GenBank extracting CDS/mRNA/translations from SWISS-PROT writing representation of to standard output features locations masking qualifiers tables of [See feature tables] field definitions DDBJ flat files EMBL flat files GenBank flat files Pfam flat files PROSITE flat files SWISS-PROT flat files files ABI sequence trace ASCII, removing carriage returns from codon usage table coordinate writing protein-heterogen contact data files from dinucleotides, counting number of domains coordinate files, writing from protein coordinate files EMBL CD-ROM format index building from BLAST database building from FASTA flat file database building from flat file database building from GCG-format database EMBL-like format, writing SCOP classification to EMBOSS data, determining directories that can hold enzymatic data of, plottng FASTA sequence entries in zzz [See also FASTA][See also FASTA] flat [See flat files] hexanucleotides, counting number of inter-chain residue-residue contact data writing intra-chain residue-residue contact data mass spectrometry result PDB, parsing profile matrix, creating from nucleic acid sequences protein coordinate writing domains coordinate files from writing from PDB files SCOP classification converting/writing to EMBL-like format files removing low-resolution domains from removing redundant domains from SWISS-PROT:PDB-equivalence, converting to EMBL-like format trinucleotides, counting number of typing sequences into findkm program (EMBOSS) flat file databases, indexing flat files DDBJ example EMBL example GenBank example Pfam example PROSITE example SWISS-PROT example flatworm mitochondrial code formatdb program formatdb program (BLAST) freak program (EMBOSS) frequency tables, codon funky program (EMBOSS) fuzznuc program (EMBOSS) fuzzpro program (EMBOSS) fuzztran program (EMBOSS) [ Team LiB ] tfscan tfscan takes a sequence and the name of one of these taxonomic groups and does a fast match of the TRANSFAC sequences against the input sequence (optionally allowing mismatches) Here is a sample session with tfscan: % tfscan Input sequence(s): embl:hsfos Transcription Factor Class F : fungi I : insect P : plant V : vertebrate O : other Select class [V]: v Number of mismatches [0]: Output file [hsfos.tfscan]: Mandatory qualifiers: [-sequence] (seqall) Sequence database USA -menu (menu) Select class -mismatch (integer) Number of mismatches [-outfile] (outfile) Output filename seqwords seqwords generates a file of hits for scop families by searching SWISS-PROT with keywords This is part of Jon Ison's protein structure analysis package This package is still being developed Please ignore this program until further details can be documented All further queries should go to Jon Ison (jison@hgmp.mrc.ac.uk) Here is a sample session with seqwords: % seqwords Mandatory qualifiers: [-keyfile] (infile) Name of keywords file (input) -spfile (infile) Name of SWISS-PROT database (input) [-outfile] (outfile) Name of seqwords hits file (output) Chapter 3 SWISS-PROT SWISS-PROT is an annotated protein sequence database that was started in 1986 It is currently overseen by the Swiss Institute of Bioinformatics (SIB) in association with the European Bioinformatics Institute (EBI) SWISS-PROT is the preferred protein sequence database for most bioinformaticians because many of the sequence annotations are curated by scientists TrEMBL, another sequence database, is a computerannotated supplement that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT It has essentially the same sequence flat file format as SWISSPROT We're using SWISS-PROT Release 40 siggen siggen parses a multiple structure alignment generated by the EMBOSS application scopalign and corresponding files of residue contact data generated by the EMBOSS application contacts and generates a protein signature of a specified sparsity Here is a sample session with siggen: % siggen Generates a sparse protein signature Location of alignment files for input [./]: /jontest Extension of alignment files for input [.align]: Location of contact files for input [./]: /jontest Extension of contact files [.con]: % sparsity of signature [10]: Generate a randomized signature [N]: Substitution matrix to be used [./EBLOSUM62]: Score alignment on basis of residue conservation [Y]: Score alignment on basis of number of contacts [Y]: Score alignment on basis of conservation of contacts [Y Score alignment on a combined measure of number and con Ignore alignment postitions with post_similar value of Name of signature file for output [sig.sig]: Mandatory qualifiers (bold if not always prompted): [-algpath] (string) Location of scop structure-based sequence alignment files (input) [-algextn] (string) Extension of alignment files -sparsity (integer) Percentage sparsity of signature -seqoption (menu) Select number -datafile (matrixf) This is the scoring matrix file used when comparing sequences -conoption (menu) Select number -filtercon (boolean) Ignore alignment positions making less than a threshold number of contacts -conthresh (integer) Threshold contact number -conpath (string) Location of contact files (input) -conextn (string) Extension of contact files -cpdbpath (string) Location of domain coordinate files (EMBL format input) -cpdbextn (string) Extension of coordinate files -filterpsim (boolean) Ignore alignment postitions with post_similar value of 0 [-sigpath] (string) Location of signature files (output) [-sigextn] (string) Extension of signature files Advanced qualifiers: -randomise (boolean) Generate a randomized signature sigscan sigscan scans a signature such as that generated by the EMBOSS application siggen against a protein sequence database and generates files of scored hits and corresponding alignments Here is a sample session with sigscan: % sigscan Mandatory qualifiers: [-sigin] (infile) Name of signature file (input) -database (seqall) Name of the SWISS-PROT sequence database to search -targetf (infile) Name of validation (input) -thresh (integer) Minimum length (residues) of overlap required for two hits with the same code to count as the same hit -sub (matrixf) This is the scoring matrix file used when comparing sequences -gapo (float) The gap insertion penalty is the score taken away when a gap is created The best value depends on the choice of comparison matrix The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences -gape (float) The gap extension penalty is added to the standard gap penalty for each base or residue in the gap This is how long gaps are penalized You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring -nterm (menu) Select number -nhits (integer) Number of hits to output [-hitsf] (outfile) Name of signature hits file (output) [-alignf] (outfile) Name of signature alignments file (output) tfextract tfextract extracts data from TRANSFAC Here is a sample session with tfextract: % tfextract Extract data from TRANSFAC Full pathname of transfac SITE.DAT: /data/transfac/site Mandatory qualifiers: [-inf] (infile) Full pathname of transfac SITE.DAT wobble wobble plots the third position variability as an indicator of a potential coding region Here is a sample session with wobble The example sequence is from Pseudomonas aeruginosa, which has a high G+C content and a very biased third codon position If it can be G or C, it usually is: % wobble Wobble base plot Input sequence: embl:paamir Graph type [x11]: Output file [paamir.wobble]: Mandatory qualifiers: [-sequence] (sequence) Sequence USA -graph (xygraph) Graph type -outf (outfile) Output filename Optional qualifiers: -window (integer) Window size in codons Advanced qualifiers: -bases (string) Bases used wordcount wordcount displays all the words of the specified length with the number of times they occur Here is a sample session with wordcount: % wordcount embl:rnu68037 -wordsize=3 Counts words of a specified size in a DNA sequence Output file [rnu68037.wordcount]: Mandatory qualifiers: [-sequence] (sequence) Sequence USA -wordsize (integer) Word size -outfile (outfile) Output filename wordmatch wordmatch finds all exact matches of a given minimum size between 2 sequences displaying the start points in each sequence and the match length Here is a sample session with wordmatch: % wordmatch tsw:hba_human tsw:hbb_human Finds all exact matches of a given size between 2 seque Word size [4]: Output alignment [hba_human.wordmatch]: Mandatory qualifiers: [-asequence] (sequence) Sequence USA [-bsequence] (sequence) Sequence USA -wordsize (integer) Word size [-outfile] (align) Output alignment filename Advanced qualifiers: -afeatout (featout) File for output of normal tab-delimited GFF features -bfeatout (featout) File for output of normal tab-delimited GFF features ... inter-chain residue-residue contact data files, writing interface program (EMBOSS) International Nucleotide Sequence Database Collaboration intra-chain residue-residue contact data files, writing invertebrate mitochondrial code... seqsearch program (EMBOSS) seqsort program (EMBOSS) sequence analysis subfields of tools for performing, list of sequence annotation sequence data lines, FASTA sequence databases MAST and table listing ways to access... [SYMBOL] [A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [Y] MAR/SAR sites, finding in nucleic acid sequences Markow models marscan program (EMBOSS) maskfeat program (EMBOSS) maskseq program (EMBOSS) mass spectrometry matching data in protein databases